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Protein

Synaptonemal complex protein 3

Gene

SYCP3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Component of the synaptonemal complexes (SCS), formed between homologous chromosomes during meiotic prophase. Required for centromere pairing during meiosis in male germ cells (By similarity). Required for normal meiosis during spermatogenesis and male fertility (PubMed:14643120). Plays a lesser role in female fertility. Required for efficient phosphorylation of HORMAD1 and HORMAD2 (By similarity).By similarity1 Publication

GO - Molecular functioni

GO - Biological processi

  • cell division Source: UniProtKB-KW
  • chiasma assembly Source: Ensembl
  • lateral element assembly Source: Ensembl
  • male meiosis I Source: UniProtKB
  • meiotic DNA repair synthesis Source: Ensembl
  • mitotic nuclear division Source: Ensembl
  • spermatogenesis, exchange of chromosomal proteins Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

Cell cycle, Cell division, Meiosis

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

ReactomeiR-HSA-1221632. Meiotic synapsis.

Names & Taxonomyi

Protein namesi
Recommended name:
Synaptonemal complex protein 3
Short name:
SCP-3
Gene namesi
Name:SYCP3
Synonyms:SCP3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 12

Organism-specific databases

HGNCiHGNC:18130. SYCP3.

Subcellular locationi

  • Nucleus By similarity
  • Chromosome By similarity
  • Chromosomecentromere By similarity

  • Note: It is present in early unpaired cores, in the lateral domains of the synaptonemal complex and in the chromosome cores when they separate at diplotene. It is found axial to the metaphase I chromosomes and in association with pairs of sister centromeres. The centromere-associated protein becomes dissociated from the centromeres at anaphase II and is not found in mitotic metaphase centromeres.By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Centromere, Chromosome, Nucleus

Pathology & Biotechi

Involvement in diseasei

Spermatogenic failure 4 (SPGF4)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionAn infertility disorder characterized by azoospermia, a condition of having no sperm present in the ejaculate. Testicular histology shows arrest of spermatogenesis at the pachytene stage of primary spermatocytes.
See also OMIM:270960

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi52 – 576KRRKKR → AAAAAA: Impairs DNA binding. Abolishes DNA binding; when associated with 88-A--A-91. 1 Publication
Mutagenesisi69 – 746EVQNML → AAAAAA: Abolishes fiber formation. 1 Publication
Mutagenesisi88 – 914KRKR → AAAA: Impairs DNA binding. Abolishes DNA binding; when associated with 52-A--A-57. 1 Publication
Mutagenesisi231 – 2366Missing : Abolishes fiber formation. 1 Publication

Organism-specific databases

MalaCardsiSYCP3.
MIMi270960. phenotype.
PharmGKBiPA38298.

Polymorphism and mutation databases

BioMutaiSYCP3.
DMDMi74728444.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 236236Synaptonemal complex protein 3PRO_0000229024Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei36 – 361PhosphoserineBy similarity
Modified residuei38 – 381PhosphoserineBy similarity
Modified residuei59 – 591PhosphoserineBy similarity

Post-translational modificationi

Phosphorylated.By similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ8IZU3.
PRIDEiQ8IZU3.

PTM databases

iPTMnetiQ8IZU3.
PhosphoSiteiQ8IZU3.

Expressioni

Tissue specificityi

Testis-specific.2 Publications

Gene expression databases

BgeeiQ8IZU3.
CleanExiHS_SYCP3.
ExpressionAtlasiQ8IZU3. baseline and differential.
GenevisibleiQ8IZU3. HS.

Organism-specific databases

HPAiCAB032978.
HPA039635.
HPA043938.

Interactioni

Subunit structurei

Component of the lateral elements of synaptonemal complexes (By similarity). Homotetramer; the tetrameric helix bundles assemble end to end into long homopolimeric fibers that exhibit a transversal striation with a periodicity of about 20 nm (in vitro) (PubMed:24950965). Interacts with SYCP2 (By similarity).By similarity1 Publication

Protein-protein interaction databases

BioGridi119081. 5 interactions.
DIPiDIP-59536N.
IntActiQ8IZU3. 1 interaction.
MINTiMINT-8303450.
STRINGi9606.ENSP00000266743.

Structurei

Secondary structure

1
236
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi71 – 777Combined sources
Helixi82 – 219138Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4CPCX-ray2.24A/B/C/D/E/F/G/H66-230[»]
ProteinModelPortaliQ8IZU3.
SMRiQ8IZU3. Positions 70-221.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni52 – 576Interaction with DNA1 Publication
Regioni69 – 746Important for oligomerization and fiber formation1 Publication
Regioni88 – 914Interaction with DNA1 Publication
Regioni231 – 2366Important for oligomerization and fiber formation1 Publication

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili66 – 223158Sequence analysis1 PublicationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi88 – 914Nuclear localization signalSequence analysis

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi105 – 232128Gln-richAdd
BLAST

Domaini

Composed of a long central coiled coil domain. The N-terminal and C-terminal regions interact with DNA.1 Publication

Sequence similaritiesi

Belongs to the XLR/SYCP3 family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiENOG410IJ2Y. Eukaryota.
ENOG4111MZD. LUCA.
GeneTreeiENSGT00390000000062.
HOGENOMiHOG000236293.
HOVERGENiHBG100390.
InParanoidiQ8IZU3.
KOiK19528.
OMAiVFQQSRI.
OrthoDBiEOG7C2R2F.
PhylomeDBiQ8IZU3.
TreeFamiTF328876.

Family and domain databases

InterProiIPR006888. XLR/SYCP3/FAM9_dom.
[Graphical view]
PfamiPF04803. Cor1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q8IZU3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVSSGKKYSR KSGKPSVEDQ FTRAYDFETE DKKDLSGSEE DVIEGKTAVI
60 70 80 90 100
EKRRKKRSSA GVVEDMGGEV QNMLEGVGVD INKALLAKRK RLEMYTKASL
110 120 130 140 150
KTSNQKIEHV WKTQQDQRQK LNQEYSQQFL TLFQQWDLDM QKAEEQEEKI
160 170 180 190 200
LNMFRQQQKI LQQSRIVQSQ RLKTIKQLYE QFIKSMEELE KNHDNLLTGA
210 220 230
QNEFKKEMAM LQKKIMMETQ QQEIASVRKS LQSMLF
Length:236
Mass (Da):27,729
Last modified:March 1, 2003 - v1
Checksum:iD871B6AEA279ABDD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF492003 mRNA. Translation: AAN06611.1.
AF517774 mRNA. Translation: AAP47204.1.
BC062662 mRNA. Translation: AAH62662.1.
CCDSiCCDS9087.1.
RefSeqiNP_001171419.1. NM_001177948.1.
NP_001171420.1. NM_001177949.1.
NP_710161.1. NM_153694.4.
UniGeneiHs.506504.

Genome annotation databases

EnsembliENST00000266743; ENSP00000266743; ENSG00000139351.
ENST00000392924; ENSP00000376655; ENSG00000139351.
ENST00000392927; ENSP00000376658; ENSG00000139351.
GeneIDi50511.
KEGGihsa:50511.
UCSCiuc001tiq.4. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF492003 mRNA. Translation: AAN06611.1.
AF517774 mRNA. Translation: AAP47204.1.
BC062662 mRNA. Translation: AAH62662.1.
CCDSiCCDS9087.1.
RefSeqiNP_001171419.1. NM_001177948.1.
NP_001171420.1. NM_001177949.1.
NP_710161.1. NM_153694.4.
UniGeneiHs.506504.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4CPCX-ray2.24A/B/C/D/E/F/G/H66-230[»]
ProteinModelPortaliQ8IZU3.
SMRiQ8IZU3. Positions 70-221.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119081. 5 interactions.
DIPiDIP-59536N.
IntActiQ8IZU3. 1 interaction.
MINTiMINT-8303450.
STRINGi9606.ENSP00000266743.

PTM databases

iPTMnetiQ8IZU3.
PhosphoSiteiQ8IZU3.

Polymorphism and mutation databases

BioMutaiSYCP3.
DMDMi74728444.

Proteomic databases

PaxDbiQ8IZU3.
PRIDEiQ8IZU3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000266743; ENSP00000266743; ENSG00000139351.
ENST00000392924; ENSP00000376655; ENSG00000139351.
ENST00000392927; ENSP00000376658; ENSG00000139351.
GeneIDi50511.
KEGGihsa:50511.
UCSCiuc001tiq.4. human.

Organism-specific databases

CTDi50511.
GeneCardsiSYCP3.
HGNCiHGNC:18130. SYCP3.
HPAiCAB032978.
HPA039635.
HPA043938.
MalaCardsiSYCP3.
MIMi270960. phenotype.
604759. gene.
neXtProtiNX_Q8IZU3.
PharmGKBiPA38298.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IJ2Y. Eukaryota.
ENOG4111MZD. LUCA.
GeneTreeiENSGT00390000000062.
HOGENOMiHOG000236293.
HOVERGENiHBG100390.
InParanoidiQ8IZU3.
KOiK19528.
OMAiVFQQSRI.
OrthoDBiEOG7C2R2F.
PhylomeDBiQ8IZU3.
TreeFamiTF328876.

Enzyme and pathway databases

ReactomeiR-HSA-1221632. Meiotic synapsis.

Miscellaneous databases

GeneWikiiSYCP3.
GenomeRNAii50511.
NextBioi53082.
PROiQ8IZU3.
SOURCEiSearch...

Gene expression databases

BgeeiQ8IZU3.
CleanExiHS_SYCP3.
ExpressionAtlasiQ8IZU3. baseline and differential.
GenevisibleiQ8IZU3. HS.

Family and domain databases

InterProiIPR006888. XLR/SYCP3/FAM9_dom.
[Graphical view]
PfamiPF04803. Cor1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A new gene family (FAM9) of low-copy repeats in Xp22.3 expressed exclusively in testis: implications for recombinations in this region."
    Martinez-Garay I., Jablonka S., Sutajova M., Steuernagel P., Gal A., Kutsche K.
    Genomics 80:259-267(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY.
  2. "A notch-related gene located on the long arm of human chromosome 12."
    Adamah D.J.B., Gokhale P.J., Walsh J., Andrews P.W., Martinez Garay I., Kutsche K.
    Submitted (JUN-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Testis.
  4. "Azoospermia in patients heterozygous for a mutation in SYCP3."
    Miyamoto T., Hasuike S., Yogev L., Maduro M.R., Ishikawa M., Westphal H., Lamb D.J.
    Lancet 362:1714-1719(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, TISSUE SPECIFICITY, INVOLVEMENT IN SPGF4.
  5. "A molecular model for the role of SYCP3 in meiotic chromosome organisation."
    Syrjanen J.L., Pellegrini L., Davies O.R.
    Elife 3:0-0(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.24 ANGSTROMS) OF 66-230, ELECTRON MICROSCOPY, SUBUNIT, DNA-BINDING, DOMAIN, REGION, MUTAGENESIS OF 52-LYS--ARG-57; 69-GLU--LEU-74; 88-LYS--ARG-91 AND 231-LEU--PHE-236.

Entry informationi

Entry nameiSYCP3_HUMAN
AccessioniPrimary (citable) accession number: Q8IZU3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 21, 2006
Last sequence update: March 1, 2003
Last modified: April 13, 2016
This is version 110 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 12
    Human chromosome 12: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.